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USGS2018

Combining genetic, isotopic, and field data to better describe the influence of dams and diversions on Burbot Movement in the Wind River Drainage, Wyoming

Dams and water diversions fragment habitat, entrain fish, and alter fish movement. Many Burbot Lota lota populations are declining, with dams and water diversions thought to be a major threat. We used multiple methods to identify Burbot movement patterns and assess entrainment into an irrigation system in the Wind River, Wyoming. We assessed seasonal movement of Burbot with a mark–recapture (PIT tagging) study, natal origins of entrained fish with otolith microchemistry, and historic movement with genotyping by sequencing. We found limited evidence of entrainment in irrigation waters across all approaches. The mark–recapture study indicated that out‐migration from potential source populations could be influenced by flow regime but was generally low. Otolith and genomic results suggested the presence of a self‐sustaining population within the irrigation network. We conclude that emigration from natural tributary populations is not the current source of the majority of Burbot found in irrigation waters. Instead, reservoir and irrigation canal construction has created novel habitat in which Burbot have established a population. Using a multi‐scale approach increased our inferential abilities and mechanistic understanding of movement patterns between natural and managed systems.

Wyoming↗

USGS2003

The Chernobyl Nuclear Power Plant accident: ecotoxicological update

The accident at the Chernobyl, Ukraine, nuclear reactor on 26 April 1986 released large amounts of radiocesium and other radionuclides into the environment, contaminating much of the northern hemisphere, especially Europe. In the vicinity of Chernobyl, at least 30 people died, more than 115,000 others were evacuated, and consumption of milk and other foods was banned because of radiocontamination. At least 14,000 human cancer deaths are expected in Russia, Belarus, and the Ukraine as a direct result of Chernobyl. The most sensitive local ecosystems, as judged by survival, were the soil fauna, pine forest communities, and certain populations of rodents. Elsewhere, fallout from Chernobyl significantly contaminated freshwater and terrestrial ecosystems and flesh and milk of domestic livestock; in many cases, radionuclide concentrations in biological samples exceeded current radiation protection guidelines. Reindeer (Rangifer tarandus) in Scandinavia were among the most seriously afflicted by Chernobyl fallout, probably because their main food during winter (lichens) is an efficient absorber of airborne particles containing radiocesium. Some reindeer calves contaminated with 137Cs from Chernobyl showed 137Cs-dependent decreases in survival and increases in frequency of chromosomal aberrations. Although radiation levels in the biosphere are declining with time, latent effects of initial exposure--including an increased frequency of thyroid and other cancers--are now measurable. The full effect of the Chernobyl nuclear reactor accident on natural resources will probably not be known for at least several decades because of gaps in data on long-term genetic and reproductive effects and on radiocesium cycling and toxicokinetics.

Book chapter↗

USGS2006

Classification tree and minimum-volume ellipsoid analyses of the distribution of ponderosa pine in the western USA

Aim? Ponderosa pine (Pinus ponderosa Douglas ex Lawson & C. Lawson) is an economically and ecologically important conifer that has a wide geographic range in the western USA, but is mostly absent from the geographic centre of its distribution - the Great Basin and adjoining mountain ranges. Much of its modern range was achieved by migration of geographically distinct Sierra Nevada (P. ponderosa var. ponderosa) and Rocky Mountain (P. ponderosa var. scopulorum) varieties in the last 10,000 years. Previous research has confirmed genetic differences between the two varieties, and measurable genetic exchange occurs where their ranges now overlap in western Montana. A variety of approaches in bioclimatic modelling is required to explore the ecological differences between these varieties and their implications for historical biogeography and impending changes in western landscapes. Location? Western USA. Methods? We used a classification tree analysis and a minimum-volume ellipsoid as models to explain the broad patterns of distribution of ponderosa pine in modern environments using climatic and edaphic variables. Most biogeographical modelling assumes that the target group represents a single, ecologically uniform taxonomic population. Classification tree analysis does not require this assumption because it allows the creation of pathways that predict multiple positive and negative outcomes. Thus, classification tree analysis can be used to test the ecological uniformity of the species. In addition, a multidimensional ellipsoid was constructed to describe the niche of each variety of ponderosa pine, and distances from the niche were calculated and mapped on a 4-km grid for each ecological variable. Results? The resulting classification tree identified three dominant pathways predicting ponderosa pine presence. Two of these three pathways correspond roughly to the distribution of var. ponderosa, and the third pathway generally corresponds to the distribution of var. scopulorum. The classification tree and minimum-volume ellipsoid model show that both varieties have very similar temperature limitations, although var. ponderosa is more limited by the temperature extremes of the continental interior. The precipitation limitations of the two varieties are seasonally different, with var. ponderosa requiring significant winter moisture and var. scopulorum requiring significant summer moisture. Great Basin mountain ranges are too cold at higher elevations to support either variety of ponderosa pine, and at lower elevations are too dry in summer for var. scopulorum and too dry in winter for var. ponderosa. Main conclusions? The classification tree analysis indicates that var. ponderosa is ecologically as well as genetically distinct from var. scopulorum. Ecological differences may maintain genetic separation in spite of a limited zone of introgression between the two varieties in western Montana. Two hypotheses about past and future movements of ponderosa pine emerge from our analyses. The first hypothesis is that, during the last glacial period, colder and/or drier summers truncated most of the range of var. scopulorum in the central Rockies, but had less dramatic effects on the more maritime and winter-wet distribution of var. ponderosa. The second hypothesis is that, all other factors held constant, increasing summer temperatures in the future should produce changes in the distribution of var. scopulorum that are likely to involve range expansions in the central Rockies with the warming of mountain ranges currently too cold but sufficiently wet in summer for var. scopulorum. Finally, our results underscore the growing need to focus on genotypes in biogeographical modelling and ecological forecasting.

Journal of Biogeography↗

USGS1985

Crystalline gold in soil and the problem of supergene nugget formation: Freezing and exclusion as genetic mechanisms

Many of the world's richest gold placer deposits now occur in cold regions despite differences in their climatic history. It therefore seems possible that there may be some fundamental connection between freezing climates and the local chemical behavior of gold in the weathering cycle. This hypothesis, along with the problematical occurrence of gold as euhedral crystals in arctic gravel and soil placers, has led me to review low temperature phenomena that may bear on the geochemistry of gold. Several effects which may influence the weathering of natural gold-bearing rocks, the chemical complexation of gold, and its subsequent mobility and deposition appear to be strongly connected with freeze action. The exclusion of dissolved solutes, solute gases, and particles from ice, subjects rock and soil minerals to increased corrosion from thin, unfrozen, adsorbed water films which remain at particle surfaces throughout the freezing of rocks and soils. The preferential exclusion of cations (over anions) from growing ice crystals creates charge separations and measurable current flow across waterice phase boundaries in freezing soil — a phenomenon which leads to troublesome seasonal electrolytic corrosion of pipelines buried in soil; this phenomenon may also favor the dissolution of normally insoluble metals such as gold during geologic time periods. The ice-induced accumulation of clays, organic acids, bacteria, and other organic matter at mineral surfaces may also speed chemical attack by providing a nearby sink of alternate cation-binding sites and hence rapid removal of liberated cations from solution. The latter mechanism may be operative in both the dissolution and redeposition of gold. These physical, chemical, and electrical effects are favorable to the dissolution of rocks (in addition to frost shattering) and to the dissolution, mobilization, and redeposition of gold and other noble metals and must therefore contribute significantly to the behavior of gold at low temperatures. The occurrence of large numbers of gold placer deposits in northern Canada, Alaska, and Siberia may thus be due in part to the low temperatures common to these regions.

Precambrian Research↗

USGS2015

Cyclic avian mass mortality in the northeastern United States is associated with a novel orthomyxovirus

Since 1998, cyclic mortality events in common eiders ( Somateria mollissima ), numbering in the hundreds to thousands of dead birds, have been documented along the coast of Cape Cod, Massachusetts, USA. Although longitudinal disease investigations have uncovered potential contributing factors responsible for these outbreaks, detecting a primary etiological agent has proven enigmatic. Here we identify a novel orthomyxovirus, tentatively named Wellfleet Bay virus (WFBV), as a potential causative agent of these outbreaks. Genomic analysis of WFBV revealed that it is most closely related to members of the Quaranjavirus genus within the family Orthomyxoviridae . Similar to other members of the genus, WFBV contains an alphabaculovirus gp64-like glycoprotein, which was demonstrated to have fusion activity, and also tentatively suggests that ticks (and/or insects) may vector the virus in nature. However, in addition to the six RNA segments encoding the prototypical structural proteins identified in other quaranjaviruses, a previously unknown RNA segment (segment 7) encoding a novel protein designated as VP7 was discovered in WFBV. Although WFBV shows low to moderate levels of sequence similarity to Quaranfil virus and Johnston Atoll virus , the original members of the Quaranjavirus genus, additional antigenic and genetic analyses demonstrated that it is closely related to the recently identified Cygnet River virus (CyRV) from South Australia, suggesting that WFBV and CyRV may be geographic variants of the same virus. Although the identification of WFBV in part may resolve the enigma of these mass mortality events, the details of the ecology and epidemiology of the virus remain to be determined. Importance The emergence or reemergence of viral pathogens resulting in large-scale outbreaks of disease in humans and/or animals is one of the most important challenges facing biomedicine. For example, understanding how orthomyxoviruses such as novel influenza A virus reassortants and/or mutants emerge to cause epidemic or pandemic disease is at the forefront of current global health concerns. Here we describe the emergence of a novel orthomyxovirus, Wellfleet Bay virus (WFBV), which has been associated with cyclic large-scale bird die-offs in the northeastern United States. This initial characterization study provides a foundation for further research into the evolution, epidemiology, and ecology of newly emerging orthomyxoviruses, such as WFBV, and their potential impacts on animal and/or human health.

Massachusets↗

USGS1989

Atlantic salmon brood stock management and breeding handbook

Anadromus runs of Atlantic salmon have been restored to the Connecticut, Merrimack, Pawcatuck, Penobscot, and St. Croix rivers in New England by the stocking of more than 8 million smolts since 1948. Fish-breeding methods have been developed that minimize inbreeding and domestication and enhance natural selection. Methods are available to advance the maturation of brood stock, control the sex of production lots and store gametes. Current hatchery practices emphasize the use of sea-run brood stock trapped upon return to the rivers and a limited number of captive brood stock and rejuvenated kelts. Fish are allowed to mature naturally, after which they are spawned and incubated artificially. Generally, 1-year smolts are produced, and excess fish are stocked as fry in headwater streams. Smolts are stocked during periods of rising water in spring. Self-release pools are planned that enable smolts to choose the emigration time. Culturists keep good records that permit evaluation of the performance of strains and the effects of breeding practices. As Atlantic salmon populations expand, culturists must use sound breeding methods that enhance biotic potential while maintaining genetic diversity and protecting unique gene pools.

Biological Report↗

USGS2007

Population response to habitat fragmentation in a stream-dwelling brook trout population

Fragmentation can strongly influence population persistence and expression of life-history strategies in spatially-structured populations. In this study, we directly estimated size-specific dispersal, growth, and survival of stream-dwelling brook trout in a stream network with connected and naturally-isolated tributaries. We used multiple-generation, individual-based data to develop and parameterize a size-class and location-based population projection model, allowing us to test effects of fragmentation on population dynamics at local (i.e., subpopulation) and system-wide (i.e., metapopulation) scales, and to identify demographic rates which influence the persistence of isolated and fragmented populations. In the naturally-isolated tributary, persistence was associated with higher early juvenile survival (-45% greater), shorter generation time (one-half) and strong selection against large body size compared to the open system, resulting in a stage-distribution skewed towards younger, smaller fish. Simulating barriers to upstream migration into two currently-connected tribuory populations caused rapid (2-6 generations) local extinction. These local extinctions in turn increased the likelihood of system-wide extinction, as tributaries could no longer function as population sources. Extinction could be prevented in the open system if sufficient immigrants from downstream areas were available, but the influx of individuals necessary to counteract fragmentation effects was high (7-46% of the total population annually). In the absence of sufficient immigration, a demographic change (higher early survival characteristic of the isolated tributary) was also sufficient to rescue the population from fragmentation, suggesting that the observed differences in size distributions between the naturally-isolated and open system may reflect an evolutionary response to isolation. Combined with strong genetic divergence between the isolated tributary and open system, these results suggest that local adaptation can 'rescue' isolated populations, particularly in one-dimensional stream networks where both natural and anthropegenically-mediated isolation is common. However, whether rescue will occur before extinction depends critically on the race between adaptation and reduced survival in response to fragmentation.

PLoS ONE↗

USGS2025

Appendix B: Patterns of bull trout Salvelinus confluentus demography, life history, abundance, and trends in the Lewis River

Declines in the distribution and abundance of bull trout ( Salvelinus confluentus ) across much of the historical range in the Pacific Northwest region of Canada and the United States have been well documented (Post and Johnston 2002; Rieman et al. 1997). Recent estimates of population trends appear to vary considerably across regions with large numbers of migratory and resident populations exhibiting substantial declines in adult abundance (Al-Chokhachy et al. 2016; Kovach et al. 2018), whereas others remain stable or potentially increasing (Erhardt and Scarnecchia 2014; Meyer et al. 2014). For example, 61% of the core populations in Alberta, Canada, are considered declining, and 39% are stable or increasing (Alberta Sustainable Resource Development 2012). The variability in population status and trends highlights the importance of population-specific data. Much of our understanding of bull trout life history has stemmed from a few, well-studied populations, and continuing to improve our knowledge of the variability in life-history expressions (e.g., Starcevich et al. 2012) can support directing local and regional conservation efforts (sensu Schindler et al. 2010). Here, we consider the life history, demographic patterns, and assess potential threats for an adfluvial population of bull trout in the upper Lewis River basin in Washington, USA. We synthesized recent monitoring efforts and field studies to refine our understanding of bull trout life-history expressions (i.e., migration patterns), demographics, and genetic status. We further evaluated the potential threats of brook trout ( S. fontinalis ), a species that is not native to the Lewis River, but which was recently documented in bull trout monitoring efforts (Al-Chokhachy et al. 2024). Our specific objectives included evaluating: (1) trends in size structure of subadults and adult bull trout (2014 – 2024); (2) patterns of adult migration and life-history and climate drivers of migration patterns (2011 – 2024); (3) the within-year temporal patterns of bull trout and coho salmon ( Oncorhynchus kisutch ) spawning and superimposition of bull trout redds by spawning coho salmon (2024); (4) temporal trends in abundance for adult and juvenile bull trout from annual monitoring methods (2008 – 2024); and (5) the current (2024) extent of non-native brook trout in wetland habitat adjacent to Yale Lake.

Washington↗

USGS2026

Genetic biocontrol strategy considerations for mosquito control in the Pacific Island Countries and Territories

Mosquito-borne diseases pose an existential threat to the health, economies, and unique ecosystems of Pacific Island Countries and Territories (PICTs). The remoteness of these islands, combined with the presence of highly competent mosquito vectors, complicates disease surveillance and vector control efforts. In response, the PICTs have become a focal point for the development and application of Genetic BioControl (GBC) technologies designed to break vector-borne disease transmission cycles. However, the application of GBC tools in this region warrants careful consideration of its unique history, including a legacy of colonialism, and challenges associated with logistic hurdles. Through meaningful community engagement and authentic collaborations, drawing from local knowledge, and building local capacity, the sustainable, efficient, and effective deployment of GBC tools may be achieved.

Current Opinion in Insect Science↗

USGS2017

Integrated wetland management for waterfowl and shorebirds at Mattamuskeet National Wildlife Refuge, North Carolina

Mattamuskeet National Wildlife Refuge (MNWR) offers a mix of open water, marsh, forest, and cropland habitats on 20,307 hectares in coastal North Carolina. In 1934, Federal legislation (Executive Order 6924) established MNWR to benefit wintering waterfowl and other migratory bird species. On an annual basis, the refuge staff decide how to manage 14 impoundments to benefit not only waterfowl during the nonbreeding season, but also shorebirds during fall and spring migration. In making these decisions, the challenge is to select a portfolio, or collection, of management actions for the impoundments that optimizes use by the three groups of birds while respecting budget constraints. In this study, a decision support tool was developed for these annual management decisions. Within the decision framework, there are three different management objectives: shorebird-use days during fall and spring migrations, and waterfowl-use days during the nonbreeding season. Sixteen potential management actions were identified for impoundments; each action represents a combination of hydroperiod and vegetation manipulation. Example hydroperiods include semi-permanent and seasonal drawdowns, and vegetation manipulations include mechanical-chemical treatment, burning, disking, and no action. Expert elicitation was used to build a Bayesian Belief Network (BBN) model that predicts shorebird- and waterfowl-use days for each potential management action. The BBN was parameterized for a representative impoundment, MI-9, and predictions were re-scaled for this impoundment to predict outcomes at other impoundments on the basis of size. Parameter estimates in the BBN model can be updated using observations from ongoing monitoring that is part of the Integrated Waterbird Management and Monitoring (IWMM) program. The optimal portfolio of management actions depends on the importance, that is, weights, assigned to the three objectives, as well as the budget. Five scenarios with a variety of objective weights and budgets were developed. Given the large number of possible portfolios (16 14 ), a heuristic genetic algorithm was used to identify a management action portfolio that maximized use-day objectives while respecting budget constraints. The genetic algorithm identified a portfolio of management actions for each of the five scenarios, enabling refuge staff to explore the sensitivity of their management decisions to objective weights and budget constraints. The decision framework developed here provides a transparent, defensible, and testable foundation for decision making at MNWR. The BBN model explicitly structures and parameterizes a mental model previously used by an expert to assign management actions to the impoundments. With ongoing IWMM monitoring, predictions from the model can be tested, and model parameters updated, to reflect empirical observations. This framework is intended to be a living document that can be updated to reflect changes in the decision context (for example, new objectives or constraints, or new models to compete with the current BBN model). Rather than a mandate to refuge staff, this framework is intended to be a decision support tool; tool outputs can become part of the deliberations of refuge staff when making difficult management decisions for multiple objectives.

North Carolina↗

USGS2024

Yosemite toad (Anaxyrus canorus) transcriptome reveals interplay between speciation genes and adaptive introgression

Genomes are heterogeneous during the early stages of speciation, with small ‘islands’ of DNA appearing to reflect strong adaptive differences, surrounded by vast seas of relative homogeneity. As species diverge, secondary contact zones between them can act as an interface and selectively filter through advantageous alleles of hybrid origin. Such introgression is another important adaptive process, one that allows beneficial mosaics of recombinant DNA (‘rivers’) to flow from one species into another. Although genomic islands of divergence appear to be associated with reproductive isolation, and genomic rivers form by adaptive introgression, it is unknown whether islands and rivers tend to be the same or different loci. We examined three replicate secondary contact zones for the Yosemite toad ( Anaxyrus canorus ) using two genomic data sets and a morphometric data set to answer the questions: (1) How predictably different are islands and rivers, both in terms of genomic location and gene function? (2) Are the adaptive genetic trait loci underlying tadpole growth and development reliably islands, rivers or neither? We found that island and river loci have significant overlap within a contact zone, suggesting that some loci are first islands, and later are predictably converted into rivers. However, gene ontology enrichment analysis showed strong overlap in gene function unique to all island loci, suggesting predictability in overall gene pathways for islands. Genome-wide association study outliers for tadpole development included LPIN3, a lipid metabolism gene potentially involved in climate change adaptation, that is island-like for all three contact zones, but also appears to be introgressing (as a river) across one zone. Taken together, our results suggest that adaptive divergence and introgression may be more complementary forces than currently appreciated.

Molecular Ecology↗

USGS2013

Distribution of Pacific lamprey Entosphenus tridentatus in watersheds of Puget Sound Based on smolt monitoring data

Lamprey populations are in decline worldwide and the status of Pacific lamprey ( Entosphenus tridentatus ) is a topic of current interest. They and other lamprey species cycle nutrients and serve as prey in riverine ecosystems. To determine the current distribution of Pacific lamprey in major watersheds flowing into Puget Sound, Washington, we sampled lamprey captured during salmonid smolt monitoring that occurred from late winter to mid-summer. We found Pacific lamprey in 12 of 18 watersheds and they were most common in southern Puget Sound watersheds and in watersheds draining western Puget Sound (Hood Canal). Two additional species, western brook lamprey ( Lampetra richardsoni ) and river lamprey ( L. ayresii ) were more common in eastern Puget Sound watersheds. Few Pacific lamprey macrophthalmia were found, suggesting that the majority of juveniles migrated seaward during other time periods. In addition, “dwarf” adult Pacific lamprey (< 300 mm) were observed in several watersheds and may represent an alternate life history for some Puget Sound populations. Based on genetic data, the use of visual techniques to identify lamprey ammocoetes as Entosphenus or Lampetra was successful for 97% (34 of 35) of the samples we evaluated.

Washington↗

USGS2019

Population estimates of Antillean manatees in Puerto Rico: An analytical framework for aerial surveys using multi-pass removal sampling

Effective management of the threatened Antillean manatee ( Trichechus manatus manatus ) in Puerto Rico requires reliable estimates of population size. Estimates are needed to assess population responses to management actions, and whether recovery objectives have been met. Aerial surveys have been conducted since 1976, but none adjusted for imperfect detection. We summarize surveys since 1976, report on current distribution, and provide population estimates after accounting for apparent detection probability for surveys between June 2010 and March 2014. Estimates in areas of high concentration (hotspots) averaged 317 ± 101, three times higher than unadjusted counts (104 ± 0.56). Adjusted estimates in three areas outside hotspots also differed markedly from counts (75 ± 9.89 versus 19.5 ± 3.5). Average minimum island-wide estimate was 386 ± 89, similar to the maximum estimate of 360 suggested in 2005, but fewer than the 700 recently suggested by the Puerto Rico Manatee Conservation Center. Manatees were more widespread than previously understood. Improving estimates, locally or island-wide, will require stratifying the island differently and greater knowledge about factors affecting detection probability. Sharing our protocol with partners in nearby islands (e.g., Cuba, Jamaica, Hispaniola), whose populations share genetic make-up, would contribute to enhanced regional conservation through better population estimates and tracking range expansion.

Puerto Rico↗

USGS2001

The interplay of species concepts, taxonomy, and conservation: lessons from the Hawaiian avifauna

The Hawaiian Islands, with their unique geological history and geographic position, provide an excellent natural laboratory in which to evaluate currently competing biological (BSC) and phylogenetic (PSC) concepts of the species. Although the BSC as historically applied in archipelagic situations is shown to be flawed in producing overlumped polytypic species, it nevertheless remains the preferable concept for most practical purposes. A review of the taxonomic history and species limits in Hawaiian birds under both concepts reveals that, when properly applied, the BSC yields a species total remarkably close to that produced under the PSC, contrary to what many proponents of the latter have supposed. We propose that the widespread adoption of the PSC for conservation purposes is potentially harmful. The PSC trivializes the species taxon and introduces new problems of deciding when a population becomes diagnosable, the possibility that species could appear and disappear in a reticulate fashion, and the likelihood that genetically diagnosable but phenotypically identical, and therefore not field identifiable, populations could be ranked as species. All of these problems negatively impact such things as constructing credible and politically defensible lists of endangered species, the prioritization of limited conservation resources, and the gathering of field data. We contend the BSC is arguably a more rational concept that better supports the activities of both scientific and nonprofessional observers. Biological species limits in oceanic archipelagoes worldwide need to be reevaluated using modern concepts and technologies before rational conservation decisions can be made.

Hawaii↗

USGS2003

Conservation genetics of North American freshwater mussels Amblema and Megalonaias

Freshwater bivalves are among the most endangered groups of organisms in North America. Efforts to protect the declining mussel fauna are confounded by ambiguities associated with recognition of distinct evolutionary entities or species. This, in part, is due to the paucity of reliable morphological characters for differentiating taxa. We have employed allozymes and DNA sequence data to search for diagnosably distinct evolutionary entities within two problematic genera of unionid mussels, Amblema and Megalonaias. Within the genus Amblema three species are recognized based on our DNA sequence data for the mitochondrial 16S rRNA and allozyme data (Amblema neislerii, A. plicata, and A. elliotti). Only one taxonomically distinct entity is recognized within the genus Megalonaias—M. nervosa. Megalonaias boykiniana of the Apalachicolan Region is not diagnosable and does not warrant specific taxonomic status. Interestingly, Megalonaias from west of the Mississippi River, including the Mississippi, exhibited an allozyme and mtDNA haplotype frequency shift suggestive of an east-west dichotomy. The results of this study eliminate one subspecies of Amblema and increase the range of A. plicata. This should not affect the conservation status of “currently stable” assigned to A. plicata by Williams et al. (1993). The conservation status of A. elliotti needs to be reexamined because its distribution appears to be limited to the Coosa River System in Alabama and Georgia.

Conservation Biology↗

USGS2014

Viruses as groundwater tracers: using ecohydrology to characterize short travel times in aquifers

Viruses are attractive tracers of short (<3 year) travel times in aquifers because they have unique genetic signatures, are detectable in trace quantities, and are mobile in groundwater. Virus “snaphots” result from infection and disappearance in a population over time; therefore, the virus snapshot shed in the fecal wastes of an infected population at a specific point in time can serve as a marker for tracking virus and groundwater movement. The virus tracing approach and an example application are described to illustrate their ability to characterize travel times in high-groundwater velocity settings, and provide insight unavailable from standard hydrogeologic approaches. Although characterization of preferential flowpaths does not usually characterize the majority of other travel times occurring in the groundwater system (e.g., center of plume mass; tail of the breakthrough curve), virus approaches can trace very short times of transport, and thus can fill an important gap in our current hydrogeology toolbox.

Ground Water↗

USGS2007

A Quantitative Threats Analysis for the Florida Manatee ( Trichechus manatus latirostris )

The Florida manatee (Trichechus manatus latirostris) is an endangered marine mammal endemic to the southeastern United States. The primary threats to manatee populations are collisions with watercraft and the potential loss of warm-water refuges. For the purposes of listing, recovery, and regulation under the Endangered Species Act (ESA), an understanding of the relative effects of the principal threats is needed. This work is a quantitative approach to threats analysis, grounded in the assumption that an appropriate measure of status under the ESA is based on the risk of extinction, as quantified by the probability of quasi-extinction. This is related to the qualitative threats analyses that are more common under the ESA, but provides an additional level of rigor, objectivity, and integration. In this approach, our philosophy is that analysis of the five threat factors described in Section 4(a)(1) of the ESA can be undertaken within an integrated quantitative framework. The basis of this threats analysis is a comparative population viability analysis. This involves forecasting the Florida manatee population under different scenarios regarding the presence of threats, while accounting for process variation (environmental, demographic, and catastrophic stochasticity) as well as parametric and structural uncertainty. We used the manatee core biological model (CBM) for this viability analysis, and considered the role of five threats: watercraft-related mortality, loss of warm-water habitat in winter, mortality in water-control structures, entanglement, and red tide. All scenarios were run with an underlying parallel structure that allowed a more powerful estimation of the effects of the various threats. The results reflect our understanding of manatee ecology (as captured in the structure of the CBM), our estimates of manatee demography (as described by the parameters in the model), and our characterization of the mechanisms by which the threats act on manatees. As an example of the type of results generated, we estimated that the probability of the manatee population falling to less than 250 adults on either the Atlantic or Gulf coasts (from a current statewide population size of near 3300) within 100 years is 8.6%. Complete removal of the watercraft threat alone would reduce this risk to 0.4%; complete removal of the warm-water threat to 4.2%; removal of both threats would reduce the risk to 0.1%. The modeling approach we have taken also allows us to consider partial removal of threats, as well as removal of multiple threats simultaneously. We believe the measure we have proposed (probability of quasi-extinction over y years, with quasi-extinction defined as dropping below a threshold of z on either coast) is a suitable measure of status that integrates a number of the elements that are relevant to interpretation under the ESA (it directly integrates risk of extinction and reduction of range, and indirectly integrates loss of genetic diversity). But the identification of the time frame of interest and the tolerable risk of quasi-extinction are policy decisions, and an ecology-based quasi-extinction threshold has not yet been determined. We have endeavored to provide results over a wide range of these parameters to give decision-makers useful information to assess status. This assessment of threats suggests that watercraft-related mortality is having the greatest impact on manatee population growth and resilience. Elimination of this single threat would greatly reduce the probability of quasi-extinction. Loss of warm-water is also a significant threat, particularly over the long-term. Red tide and entanglement, while noticeable threats, have had less of an impact on the manatee population. The effect of water control structures may have already been largely mitigated. We did not, however, consider an exhaustive list of threats. Other threats (e.g., reduction of food resources due to storms and development) may play a

Open-File Report↗

USGS2020

Ambiguities in using telomere length for age determination in two North American bat species

The age of an animal, determined by time (chronological age) as well as genetic and environmental factors (biological age), influences the likelihood of mortality and reproduction and thus the animal’s contribution to population growth. For many long-lived species, such as bats, a lack of external and morphological indicators has made determining age a challenge, leading researchers to examine genetic markers of age for application to demographic studies. One widely studied biomarker of age is telomere length, which has been related both to chronological and biological age across taxa, but only recently has begun to be studied in bats. We assessed telomere length from the DNA of known-age and minimum known-age individuals of two bat species using a quantitative PCR assay. We determined that telomere length was quadratically related to chronological age in big brown bats ( Eptesicus fuscus ), although it had little predictive power for accurate age determination of unknown-age individuals. The relationship was different in little brown bats ( Myotis lucifugus ), where telomere length instead was correlated with biological age, apparently due to infection and wing damage associated with white-nose syndrome. Furthermore, we showed that wing biopsies currently are a better tissue source for studying telomere length in bats than guano and buccal swabs; the results from the latter group were more variable and potentially influenced by storage time. Refinement of collection and assessment methods for different non-lethally collected tissues will be important for longitudinal sampling to better understand telomere dynamics in these long-lived species. Although further work is needed to develop a biomarker capable of determining chronological age in bats, our results suggest that biological age, as reflected in telomere length, may be influenced by extrinsic stressors such as disease.

Journal of Mammalogy↗